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Near‐shore microbial communities (Eukaryotes, Bacteria and Archaea) of the sub‐Antarctic Prince Edward Islands

Latest version published by SCAR - Microbial Antarctic Resource System on Dec 12, 2018 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset of microbial eukaryotes (18S ssh rRNA); bacteria (16S) and Archaea (16S) from coastal seawater near the shore of the Prince Edward Islands (Indian Ocean, Sub-Antarctica); sampled from a single location (37.58 degrees South 46.36 degrees East) in 2012, 2013, 2014 and 2015.

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How to cite

Researchers should cite this work as follows:

Venkatachalam S, Matcher G, Lamont T, Dorrington R (2018): Near‐shore microbial communities (Eukaryotes, Bacteria and Archaea) of the sub‐Antarctic Prince Edward Islands. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. http://ipt.biodiversity.aq/resource?r=marine_microbial_communities_princeeedward_islands&v=1.0

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 576f1f95-2ad4-4d23-a052-c02d901929f1.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata

Contacts

Who created the resource:

Siddarthan Venkatachalam
Post doctoral researcher
Rhodes University Grahamstown ZA
Gwynneth Matcher
Research fellow
Rhodes University Grahamstown ZA
Tarron Lamont
Research associate
Department of Environmental Affairs Cape Town ZA
Rosemary Dorrington
Professor
Rhodes University Grahamstown ZA

Who can answer questions about the resource:

Rosemary Dorrington
Professor
Rhodes University Grahamstown ZA

Who filled in the metadata:

Maxime Sweetlove
Research assistent
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels BE

Who else was associated with the resource:

User

Geographic Coverage

Sampled near the Prince Edward Islands (Indian Ocean, Sub-Antarctica); 37.58 degrees South 46.36 degrees East

Bounding Coordinates South West [-37.58, 46.36], North East [-37.58, 46.36]

Taxonomic Coverage

Microbial Eukaryotes (18S ssh rRNA gene, v9), Bacteria (16S ssh rRNA gene, v4-v5) and Archaea (16S ssh rRNA gene, v4-v5)

Domain  Eukaryota (Eukaryotes),  Bacteria (Bacteria),  Archaea (Archaea)

Temporal Coverage

Formation Period 2012-2015

Project Data

No Description available

Title Influence of oceanographic variability on near‐shore microbial communities
Funding This project was funded by grants from the South African National Antarctic Programme (SANAP) through the South African National Research Foundation (NRF) to R.A.D. (80260) and I.J.A. (80270) and the Rhodes University Sandisa Imbewu Programme; the DST/NRF SARChI Post‐Doctoral Fellowship (87583); the South African Department of Environmental Affairs (DEA) and the University of Cape Town and Rhodes University.

The personnel involved in the project:

Siddarthan Venkatachalam

Sampling Methods

Two liters of surface (5 m depth) seawater was initially filtered through 100 μm mesh to remove particulate matter, after which microbial biomass was collected by filtration through 0.22 μm Polyethersulfone (PES) membrane (Pall Corporation). The filters were immersed in RNALater (Qiagen) and stored at −20°C.

Study Extent Seawater samples were collected at a near‐shore site on the northeast coast of PEI at 46°36.415′S; 37°58.553′E during the austral autumn (April) and winter (July) seasons in 2012 as well as the austral autumn (May) for years 2013, 2014, and 2015.

Method step description:

  1. Genomic DNA (gDNA) and RNA were extracted from PES filters using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer's instructions. For the rRNA sequencing, isolated RNA was converted to cDNA using the QuantiTect Reverse Transcription Kit (Qiagen) according to the manufacturer's protocol. For the analysis of bacterial community composition, the V4‐V5 variable regions of the bacterial 16S rRNA gene were amplified by PCR using the E517F (5′‐CAG CAG CCG CGG TAA‐3′) and E969‐984R (5′‐GTA AGG TTC YTC GCG T‐3′) primers) with suitable multiplex identifier tags and sequencing primer binding sites attache. For the analysis of eukaryotic phytoplankton community diversity, PCR amplification of 18S rRNA gene sequences was carried out using primers 1391F: 5′‐GTA CAC ACC GCC CGT C‐3′ (Saccharomyces cerevisiae position 1629–1644) and EukB: 5′‐TGA TCC TTC TGC AGG TTC ACC TAC‐3′ (S. cerevisiae position 1774–1797) targeting the V9 regions of the eukaryotic SSU rRNA. Archaeal 16S rRNA gene sequences (V4‐V5 variable regions) were amplified using pr514–528: 5′‐GGT GYC AGC CGC CGC‐3′ and A906R: 5’‐CCC GCC AAT TCC TTT AAG TTTC‐3, respectively.
  2. PCR amplification of the bacteria, phytoplankton and archaeal gene fragments was carried out in a 25 μL reaction volume comprising 10 ng of the extracted DNA and using KAPAHiFi Hotstart DNA Polymerase (KAPA Biosystems) according to the manufacturer's instructions. For bacterial 16S rRNA gene amplification, the reaction mixtures were subjected to the reaction conditions described in Matcher et al. (2011). For 18S rRNA amplification, the PCR cycling parameters were as follows: 98°C (45 s), 57°C (30 s), 72°C (45 s) for five cycles, 98°C (45 s), 65°C (30 s), and 72°C (45 s) for 15 cycles and a final extension at 72°C for 5 min. For archaeal 16S rRNA gene amplification, cycling conditions were used as for the 18S rRNA amplification with amendments of the annealing temperatures to 56°C (30 s) for the first five cycles and 59°C (30 s) for next 15 cycles.
  3. The PCR amplification products were gel‐purified using the ISOLATE II PCR and Gel Kit (Bioline), subjected to emulsion PCR, and then sequenced using the GS Junior Titanium Sequencer (454 Life Sciences, Roche).

Bibliographic Citations

  1. Venkatachalam, S., Matcher, G. F., Lamont, T., van den Berg, M., Ansorge, I. J., & Dorrington, R. A. (2018). Influence of oceanographic variability on near‐shore microbial communities of the sub‐Antarctic Prince Edward Islands. Limnology and Oceanography.